During the Mississippian Period 345 million years ago, the southwest United States was covered by ocean. Skeletons of sea life settling to the depths, created a mud with a high percentage of calcium. This eventually hardened into the limestone bedrock seen in the caverns today. Over millions of years, the bedrock was pushed up to over 5,000 feet (1,500 m) above sea level.

Approximately 35 million years ago, rainfall flowed into the rock, and eroded passages that lead to theColorado River and what is now the Grand Canyon. Millions of years later, the evaporating water left calcium deposits on the walls and floors, creating the formations that can be viewed today.

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In 1927, cowboy and woodcutter Walter Peck was walking through the area on his way to play poker with his friends when he stumbled and nearly fell into a hole. Peck and some of his friends returned the next day to the large, funnel shaped hole with lanterns and ropes. With a rope tied around his waist, he was lowered into the hole to a depth of 150 feet (46 m), and began exploring.

Speckles on the walls led Peck to think he had discovered a gold mine. He gathered samples of the shiny rocks and had his friends pull him back to the surface. He then purchased the property and began making preparations for a gold mining operation. But once the assay reports were completed, he learned that his potential mother lode was nothing more than iron oxide.

Not one to give up on entrepreneurial opportunities, Peck decided to open the caverns to travelers and began charging 25 cents to lower these early cavers down into the caverns, where they were able to view what had been reported to be the remains of a caveman located on a ledge. Although the 'caveman' had also brought scientists from the east to study the remains, in the 1960s the "caveman" was shown to be the remains of two inhabitants of the area. These men had died in the winter of 1917-1918, barely a decade before the caverns' discovery. Part of a group of Hualapai Native Americans harvesting and cutting firewood on the caverns' hilltop, they were trapped there for three days by a snowstorm. Two brothers died from influenza, and since the ground was frozen solid with and covered in snow, they were buried in what was thought to be only a 50-foot (15 m) hole, as returning them to their tribal headquarters in Peach Springs risked spreading the flu.

In 1935, the Civilian Conservation Corps and the Works Progress Administration made an agreement with Peck to build a new entrance to the Caverns. In 1962, another entrance was built by blasting a 210-foot (64 m) shaft into the limestone and installing a large elevator. At that time the natural entrance was also sealed off at the request of the Hualapai Indians as it was considered a sacred burial place. Near the natural entrance, the skeletal remains of a Paramylodon harlani (Glossotherium harlani) were also found. This giant and extinct ground sloth lived during the Age of Mammals around 11,000 years ago, when the woolly mammoth and saber tooth cat roamed North America.

Peck had named the caverns Yampai Caverns, with the name being changed several times. Up until 1957, they were known as The Coconino Caverns. From 1957 through 1962, they were known as The Dinosaur Caverns and there are plenty of contemporary but artificial 'dinosaur' artifacts from this era that exist to this day. In 1962, they were renamed The Grand Canyon Caverns, as they are connected to the Grand Canyon to the north.

During the 1962 Cuban Missile Crisis, the U.S. government deployed enough water and food rations to the caverns to support 2,000 people for up to two weeks. These supplies remain there today and are seen by visitors who tour the caverns. But a more interesting fact is that these supplies are still as ready to eat and drink as they were when deployed due to the constant dryness and cool temperature of the air inside.

Not simply a Historic Route 66 roadside tourist attraction, the caverns are the location of ongoing scientific work related not only to cave exploration, but to space exploration as well. A cosmic ray telescope was installed in 1979 under 126 feet (38 m) of solid limestone by the Department of Physics and Astronomy of the University of New Mexico. The purpose of the telescope is to study interstellar cosmic rays that constantly bombard the earth from deep space, penetrating solid rock.

The Grand Canyon Caverns are the largest dry caverns in the United States and may be the largest dry cavern system on earth. At a constant 57 °F (14 °C) with only 2 percent humidity year round, the caverns are an ideal preservation area.

Cavers and tourists alike can take a 45-minute, guided, walking tour of the caverns beginning with a 21-story, or 210-foot (64 m) descent in an elevator from the surface, or a shorter 25-minute wheelchair-accessible tour. With proper permission, more hardcore and professional cavers are allowed to explore areas that are not seen on the scheduled tours.

The first cavern after leaving the elevator is the Chapel of the Ages, which is large enough to hold up to two football fields. Numerous weddings have been performed here. The most popular guided walking tour is about 0.75 miles (1.21 km) long through winding, natural tunnels where helecite crystals, a rather rare form of selenite, red-wall limestone, 'teacup handles', 'winter crystals' and more can be seen. Also on this tour are the large cache of cold-war-era rations placed there in the 1960s.

A hotel, (The Grand Canyon Caverns Inn), an RV park, campgrounds, a restaurant, a convenience store, and a 5,100-foot (1,600 m) runway, all located along the longest remaining, contiguous stretch of historic Route 66, enable visitors to arrive by plane or vehicle and stay to explore, both the underground and above-ground features, as long as desired. The Elderhostel organization offers several travel adventures to the resort.

Located on the Coconino Plateau, just a few miles west of the Aubrey Cliffs that rise to over 6,100 feet (1,900 m) above sea level, the Caverns lie within an alluvial plain at an altitude of about 5,300 feet (1,600 m). Limestone comprises the majority of the subsurface area of this vicinity of the Coconino Plateau, an area riddled with numerous cavernous veins that run for miles in all directions. During the 1950s, scientists began searching for the source of fresh air encountered in the cavern's depths. It is said that the engineers set off red flares in the Snowball cavern room and once it dissipated they searched for many days in the surrounding countryside for signs of seepage from the earth's surface, but no smoke was ever seen. It is said[who?] that a few weeks afterward rangers who worked at Grand Canyon National Park reported seeing red smoke seeping from the rocks in the canyon walls nearly 63 miles (101 km) to the north of the Caverns close by the village of Supai.